Package csb :: Package bio :: Package sequence :: Module alignment :: Class SimilarityMatrix

Class SimilarityMatrix

           object --+    
                    |    
AbstractScoringMatrix --+
                        |
                       SimilarityMatrix

Similarity scoring matrix.

Nested Classes
Inherited from `AbstractScoringMatrix`: `__metaclass__`

Instance Methods

__init__(self, matrix={'*': {'*': 1.0, 'A': -4.0, 'B': -4.0, 'C': -4.0, 'D': -4.0, '...)
x.__init__(...) initializes x; see help(type(x)) for signature source code

float

score(self, x, y)
Return the pairwise score of residues x and y. source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

SimilarityMatrix

parse(string)
Parse a standard scoring matrix file, where the first row and column are residue labels.

source code

Class Variables
	BLOSUM62 = `{'': {'': 1.0, 'A': -4.0, 'B': -4.0, 'C': -4.0, '...`
	__abstractmethods__ = `frozenset([])`

Properties
Inherited from `object`: `__class__`

Method Details

init(self, matrix=`{'':` `{'':` 1.0`,` `'A':` -4.0`,` `'B':` -4.0`,` `'C':` -4.0`,` `'D':` -4.0`,` `'...`)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

matrix

Overrides: object.__init__

(inherited documentation)

parse(string)
Static Method

source code

Parse a standard scoring matrix file, where the first row and column are residue labels.

Parameters:

string (str) - scoring matrix string

Returns: SimilarityMatrix

score(self, x, y)

source code

Return the pairwise score of residues x and y. x and y must be comparable (e.g. implement __eq__ and __hash__).

Parameters:

x - first residue
y - second residue

Returns: float

Raises:

ResidueNotFoundError - if x or y cannot be handled by this scoring matrix

Overrides: AbstractScoringMatrix.score

(inherited documentation)

Class Variable Details

BLOSUM62

Value:

{'*': {'*': 1.0,
       'A': -4.0,
       'B': -4.0,
       'C': -4.0,
       'D': -4.0,
       'E': -4.0,
       'F': -4.0,
       'G': -4.0,
...

Class SimilarityMatrix

__init__(self, matrix={'*': {'*': 1.0, 'A': -4.0, 'B': -4.0, 'C': -4.0, 'D': -4.0, '...) (Constructor)

parse(string) Static Method

score(self, x, y)

BLOSUM62

init(self, matrix=`{'':` `{'':` 1.0`,` `'A':` -4.0`,` `'B':` -4.0`,` `'C':` -4.0`,` `'D':` -4.0`,` `'...`)
(Constructor)

parse(string)
Static Method